There are several reptile species of conservation significance in this ecoregion, including the monitor lizard (Varanus salvator), the false gavial (Tomistoma schlegeli), and the estuarine crocodile (Crocodylus porosus).

It also has hybrids of the two, as well as the indigenous false gavial (Tomistoma schlegelii) and five exotic species: South American caiman (Caiman crocodilus), New Guinea freshwater crocodile (Crocodylus novaeguineae), Chinese alligator (Alligator sinensis), broad-spouted caiman

In 1974 an FAO report on India's crocodiles noted that the Indian gavial (Gavialis gangeticus) was on the verge of extinction, the saltwater crocodile was extremely rare, and the Indian mugger (Crocodylus palustris was a depleted, although not threatened, species).